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Published 20 hours ago • verified publisher icon broadinstitute

SNVQ recalibration for flow based reads

Open ilyasoifer opened this issue 1 year ago • 1 comments

ilyasoifer avatar Feb 16 '24 14:02 ilyasoifer

@ilyasoifer Tool has been renamed to AddFlowSNVQuality (as to be similar to existing AddFlowBaseQuality). Model (and related conf) removed.

dror27 avatar Feb 26 '24 08:02 dror27

@meganshand - this should be ready for your review, there is a parallel PR in picard that adds tools that can collect statistics from the output of this tool, so would be good to merge this one first Thanks a lot!

ilyasoifer avatar Mar 12 '24 19:03 ilyasoifer

@meganshand - thank you for your comments. I have responded and updated. We have just a few left between @ilyasoifer and myself - then you can have it back for another round.

dror27 avatar Mar 25 '24 08:03 dror27

@dror27 - I addressed the comments that were assigned to me. There is some documentation task left and that failing test and then we are ready, I think.

ilyasoifer avatar Mar 28 '24 20:03 ilyasoifer

@dror27 - I addressed the comments that were assigned to me. There is some documentation task left and that failing test and then we are ready, I think.

I'm finding out that the failing test is due to different floating point accuracy between the platform on which the expected file is generated and the one running the test. I will change the way the expected and generated files are changed against to accommodate for that

 -5.695667472802612
> -5.695667472802612
> -5.695667472802612

dror27 avatar Mar 31 '24 09:03 dror27

@meganshand - I think that we addressed all your comments, could you take another look please?

ilyasoifer avatar Mar 31 '24 12:03 ilyasoifer